R/methods-plotViolin.R

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

#' Plot Violin
#'
#' @name plotViolin
#' @family Gene Expression Functions
#' @author Michael Steinbaugh
#'
#' @importFrom bcbioBase plotViolin
#'
#' @inheritParams general
#' @inheritParams ggplot2::geom_violin
#'
#' @seealso [Seurat::VlnPlot()].
#'
#' @return `ggplot`.
#'
#' @examples
#' # seurat ====
#' object <- seurat_small
#' genes <- head(rownames(object), 4L)
#' plotViolin(object, genes = genes)
NULL



# Methods ======================================================================
#' @rdname plotViolin
#' @export
setMethod(
    "plotViolin",
    signature("SingleCellExperiment"),
    function(
        object,
        genes,
        scale = c("count", "width", "area"),
        fill = NULL,
        legend = FALSE
    ) {
        scale <- match.arg(scale)
        assert_is_any_of(fill, c("ScaleDiscrete", "character", "NULL"))
        if (is.character(fill)) {
            assert_is_a_string(fill)
        }

        ident <- slot(object, "ident")
        data <- fetchGeneData(object, genes = genes) %>%
            as.data.frame() %>%
            cbind(ident) %>%
            rownames_to_column("cell") %>%
            as_tibble() %>%
            gather(
                key = "gene",
                value = "expression",
                !!genes
            ) %>%
            group_by(!!sym("gene"))

        violin <- geom_violin(
            mapping = aes_string(fill = "ident"),
            # never include a color border
            color = "black",
            scale = scale,
            adjust = 1L,
            show.legend = legend,
            trim = TRUE
        )
        if (is_a_string(fill)) {
            violin[["aes_params"]][["fill"]] <- fill
        }

        p <- ggplot(
            data,
            mapping = aes_string(
                x = "ident",
                y = "expression"
            )
        ) +
            violin +
            # Note that `scales = free_y` will hide the x-axis for some plots
            facet_wrap(facets = "gene", scales = "free_y")

        if (is(fill, "ScaleDiscrete")) {
            p <- p + fill
        }

        p
    }
)



#' @rdname plotViolin
#' @export
setMethod(
    "plotViolin",
    signature("seurat"),
    getMethod("plotViolin", "SingleCellExperiment")
)